[gmx-users] Extending simulation problem.

[Dawid das]

Oh I forgot that I used -append option in the latter \$MDRUN command:

\$MDRUN -s npt-md-ext.tpr -cpi state.cpt -append




2014-08-20 11:33 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> Dear Gromacs experts,
>
> I googled for answer and I found these:
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_10000_ps
>
> but still I am confused about what happens in my simulation. I did 5 ns
> simulation and I would like to add extra 5 ns on top of that so that new
> results (energies, temperature, trajectory, etc.) will be appended to
> already existing files after first 5 ns simulation. Now I used this command
> to run MD simulation for the first time:
>
> \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e
> mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1
>
> After this in the same directory I run:
>
> tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr
>
> \$MDRUN -s npt-md-ext.tpr -cpi state.cpt
>
> I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same
>
> that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of
>
> previous simulation. What can cause that? Is it because of used files names or I did something else wrong?
>
> Best wishes,
>
> Dawid Grabarek
>
>